Recognizing the value of software: a software citation guide.

Software is as integral as a research paper, monograph, or dataset in terms of facilitating the full understanding and dissemination of research. This article provides broadly applicable guidance on software citation for the communities and institutions publishing academic journals and conference proceedings. We expect those communities and institutions to produce versions of this document with software examples and citation styles that are appropriate for their intended audience. This article (and those community-specific versions) are aimed at authors citing software, including software developed by the authors or by others. We also include brief instructions on how software can be made citable, directing readers to more comprehensive guidance published elsewhere. The guidance presented in this article helps to support proper attribution and credit, reproducibility, collaboration and reuse, and encourages building on the work of others to further research.

20 years of ultrasound contrast agent modeling.

The merits of ultrasound contrast agents (UCAs) were already known in the 1960s. It was, however, not until the 1990s that UCAs were clinically approved and marketed. In these years, it was realized that the UCAs are not just efficient ultrasound scatterers, but that their main constituent, the coated gas microbubble, acts as a nonlinear resonator and, as such, is capable of generating harmonic energy. Subharmonic, ultraharmonic, and higher harmonic frequencies of the transmitted ultrasound frequency have been reported. This opened up new prospects for their use and several detection strategies have been developed to exploit this harmonic energy to discriminate the contrast bubbles from surrounding tissue. This insight created a need for tools to study coated bubble behavior in an ultrasound field and the first models were developed. Since then, 20 years have elapsed, in which a broad range of UCAs and UCA models have been developed. Although the models have helped in understanding the responses of coated bubbles, the influence of the coating has not been fully elucidated to date and UCA models are still being improved. The aim of this review paper is to offer an overview in these developments and indicate future directions for research.

Acoustical properties of individual liposome-loaded microbubbles.

A comparison between phospholipid-coated microbubbles with and without liposomes attached to the microbubble surface was performed using the ultra-high-speed imaging camera (Brandaris 128). We investigated 73 liposome-loaded microbubbles (loaded microbubbles) and 41 microbubbles without liposome loading (unloaded microbubbles) with a diameter ranging from 3-10 µm at frequencies ranging from 0.6-3.8 MHz and acoustic pressures ranging from 5-100 kPa. The experimental data showed nearly the same shell elasticity for the loaded and unloaded bubbles, but the shell viscosity was higher for loaded bubbles compared with unloaded bubbles. For loaded bubbles, a higher pressure threshold for the bubble vibrations was noticed. In addition, an "expansion-only" behavior was observed for up to 69% of the investigated loaded bubbles, which mostly occurred at low acoustic pressures (≤30 kPa). Finally, fluorescence imaging showed heterogeneity of liposome distributions of the loaded bubbles.

Brandaris 128 ultra-high-speed imaging facility: 10 years of operation, updates, and enhanced features.

The Brandaris 128 ultra-high-speed imaging facility has been updated over the last 10 years through modifications made to the camera's hardware and software. At its introduction the camera was able to record 6 sequences of 128 images (500 × 292 pixels) at a maximum frame rate of 25 Mfps. The segmented mode of the camera was revised to allow for subdivision of the 128 image sensors into arbitrary segments (1-128) with an inter-segment time of 17 µs. Furthermore, a region of interest can be selected to increase the number of recordings within a single run of the camera from 6 up to 125. By extending the imaging system with a laser-induced fluorescence setup, time-resolved ultra-high-speed fluorescence imaging of microscopic objects has been enabled. Minor updates to the system are also reported here.

In vivo characterization of ultrasound contrast agents: microbubble spectroscopy in a chicken embryo.

The dynamics of coated microbubbles was studied in an in vivo model. Biotinylated lipid-coated microbubbles were prepared in-house and were injected into a chick embryo chorioallantoic membrane (CAM) model on the fifth day of incubation. The microbubbles, ranging between 1.0 and 3.5 µm in diameter, were insonified in the frequency range of 4-7 MHz. Two amplitudes of acoustic pressure were applied: 300 kPa and 400 kPa. The fundamental and subharmonic responses were recorded optically with an ultra-fast camera (Brandaris 128) at 20 million frames per second. A subharmonic response was observed for 44% of the studied bubbles. From the data the frequency of the maximum fundamental and subharmonic response was derived for each individual bubble and resulted in the resonance curves of the microbubbles. All the bubbles showed shell (strain) hardening behavior for a higher acoustic pressure. We conclude that the subharmonic oscillations observed in this study belonged to the transmit at resonance (TR) regime.

Dynamic manipulation of the subharmonic scattering of phospholipid-coated microbubbles.

In this paper, the influence of a dynamic variation in the ambient pressure on the subharmonic response of phospholipid-coated microbubbles was investigated. The ambient pressure in water was modulated by a 2.5 kHz acoustic wave with a peak amplitude of 15 kPa. We investigated the fundamental and subharmonic emissions at two driving frequencies: 5 and 10 MHz. The modulation of the bubble radius induced by the dynamic variation in the liquid ambient pressure subsequently causes modulations of the scattered acoustic pressure at the fundamental and subharmonic frequencies (half the fundamental frequency). As a first result, we measured that the variation in the ambient pressure of 15 kPa can modulate the subharmonic amplitude up to 10 dB as compared to the static atmospheric pressure condition. As a second result, we noticed that the relative subharmonic amplitude modulation as a function of the LF acoustic pressure was symmetrical for the 5 MHz driving frequency but asymmetric for 10 MHz. In the latter case, the subharmonic amplitude was more enhanced for an ambient overpressure than reduced for an ambient depression of the same amplitude likely due to the buckling of the lipid shell. However, the fundamental amplitude was symmetrically modulated during bubble compression and expansion. Moreover, subharmonic and fundamental amplitude modulations were found to be either in phase or out of phase with the low-frequency acoustic pressure. Numerical simulations showed that this behavior can be obtained depending on the bubbles' diameter. The highest subharmonic amplitude was measured when microbubbles were insonified at 10 MHz. This fact together with the asymmetry observed in the subharmonic modulation suggests that smaller bubbles with a buckling shell are excited at 10 MHz compared to 5 MHz. These results present new potentials for in vitro characterization of contrast agent microbubbles and possibly a new imaging modality.

Second harmonic inversion for ultrasound contrast harmonic imaging.

Ultrasound contrast agents (UCAs) are small micro-bubbles that behave nonlinearly when exposed to an ultrasound wave. This nonlinear behavior can be observed through the generated higher harmonics in a back-scattered echo. In past years several techniques have been proposed to detect or image harmonics produced by UCAs. In these proposed works, the harmonics generated in the medium during the propagation of the ultrasound wave played an important role, since these harmonics compete with the harmonics generated by the micro-bubbles. We present a method for the reduction of the second harmonic generated during nonlinear-propagation-dubbed second harmonic inversion (SHI). A general expression for the suppression signals is also derived. The SHI technique uses two pulses, p' and p″, of the same frequency f(0) and the same amplitude P(0) to cancel out the second harmonic generated by nonlinearities of the medium. Simulations show that the second harmonic is reduced by 40 dB on a large axial range. Experimental SHI B-mode images, from a tissue-mimicking phantom and UCAs, show an improvement in the agent-to-tissue ratio (ATR) of 20 dB compared to standard second harmonic imaging and 13 dB of improvement in harmonic power Doppler.

Characterizing the subharmonic response of phospholipid-coated microbubbles for carotid imaging.

The subharmonic vibration of BR14 (Bracco Research S.A., Geneva, Switzerland) contrast agent microbubbles is investigated within the preferable frequency range for carotid ultrasound imaging (8-12 MHz). The response of the bubbles was recorded optically with an ultra-fast recording camera (Brandaris 128) at three acoustic pressures (50, 100 and 120 kPa). The vibration of the microbubbles was measured as a function of the excitation frequency and its frequency content was determined. Among 390 recordings, 40% showed subharmonic oscillations. It was observed that for smaller microbubbles (diameter < 3 µm) the frequency of the maximum subharmonic response increases for increasing pressures (shell hardening) opposite to what has been reported for larger microbubbles (3 µm < diameter < 15 µm). These findings are well predicted by the model proposed by Marmottant et al. (2005) after including the dilatational shell viscosity of the microbubbles measured by Van der Meer et al. (2007), which indicates a marked shear-thinning behavior of the phospholipid shell.

Characterization of Definity™ ultrasound contrast agent at frequency range of 5-15 MHz.

The status of vasa vasorum, which can be imaged using ultrasound contrast agents, is an indication for the progression of atherosclerosis. The preferred ultrasound frequency for this purpose is between 5 and 15 MHz. Therefore, it is essential to have knowledge about the acoustic properties of microbubbles such as elasticity and viscosity to be able to implement the current models for lipid encapsulated microbubbles developed for frequencies used in precordial imaging. In this study, the shell parameters, stiffness S(p) and friction S(f), of Definity™ microbubbles have been calculated at frequency range of 5-15 MHz by comparing the theoretical modeling of acoustic bubble response and experimental measurements. Derived parameters are in good agreement with previous estimations on SonoVue™ and Sonazoid™ contrast agent. However, the value of S(f) is higher than previously estimated for Definity™ between 12-28 MHz.